heterozygousSNPs {beadarraySNP} | R Documentation

## Retrieve heterozygous SNPs

### Description

Heterozygous SNPs are determined based on quality score criteria

### Usage

      heterozygousSNPs(object, threshold=0.9, useQuality=TRUE, relative=TRUE,
                       percentile=FALSE)

### Arguments

`object` | class SnpSetIllumina
`threshold` | numeric (0:1) minimum quality score to be called heterozygous
`useQuality` | logical, use quality score
`relative` | logical, use quality score relative to GTS, see details
`percentile` | logical, use percentage of probes above threshold

### Details

This function presumes that the specificity for determining heterozygity is more important than the sensitivity, and will therefore only call probes heterozygous if that can be done with high certainty.
The Illumina genotyping software calculates two quality measures: gen train score (GTS) and gen call score (GCS). The GTS is a measure for how well clusters can be recognized in a training set. This value is probe specific, and the same for all samples in an experiment. The GCS is a probe-specific, sample specific value that measures how close a probe in a sample is to the clusters determined in the training step. This value is always lower than the GTS for a probe.
`read.SnpSetIllumina` will put GCS into the `callProbability` element of the `assaydata` slot and the GTS into the `featureData` slot. The function uses these locations to retrieve the necessary information.
If `relative` is `FALSE` then the raw GCS values are compared to the `threshold`. In this case a `threshold` of around 0.5 should be used. If `relative` is `TRUE` then GCS/GTS is compared to the `threshold` and `threshold` should be around 0.9.
With `percentile=TRUE` the `threshold` quantile is calculated for each sample, and only probes with higher scores can be called heterozygous. A `threshold` of around 0.2 seems to work fine usually.

### Value

This function returns a `logical matrix` with same dimensions as `object`.

### Note

The purpose of the function is to separate heterozygous probes from non-heterozygous probes. In tumor samples the determination of the genotype can be difficult, because of aneuploidy and the fact that a sample is often a mixture of normal and tumor cells.

### Author(s)

Jan Oosting

### See Also

`SnpSetIllumina-class`

### Examples

      data(chr17.260)
      plot(heterozygosity(heterozygousSNPs(chr17.260[,"514TV"])),col="red",pch="x")
      points(heterozygosity(exprs(chr17.260)[,"514TV"]))

[Package beadarraySNP version 1.60.0 Index]